Genetic testing for predicting resistance of salmonella species against antimicrobial agents

Abstract

The invention relates to a method of determining an infection of a patient with Salmonella species potentially resistant to antimicrobial drug treatment, a method of selecting a treatment of a patient suffering from an antibiotic resistant Salmonella infection, and a method of determining an antibiotic resistance profile for bacterial microorganisms of Salmonella species, as well as computer program products used in these methods. In an exemplary method, a sample 1 is used for molecular testing 2, and then a molecular fingerprint 3 is taken. The result is then compared to a reference library 4, and the result 5 is reported.

1 . A diagnostic method of determining an infection of a patient with  Salmonella  species potentially resistant to antimicrobial drug, e.g. antibiotic, treatment, comprising the steps of:
 a) obtaining or providing a sample containing or suspected of containing at least one  Salmonella  species from the patient;   b) determining the presence of at least one mutation in at least two genes from the group of genes consisting of recN, hemH, UMN798_3428, metE, yijD, UMN798_4831, UMN798_1939, copS, UMN798_0628, UMN798_4878, leuB, recF, emrA, glyQ, dcp, thiH, UMN798_1612, UMN798_2909, UMN798_1680, UMN798_4073, yjbC, nadB, UMN798_3160, hutU, envC, UMN798_3889, UMN798_1629, bcfB, degQ, UMN798_1331, trg, uvrC, polB, hpcD, UMN798_1628, UMN798_1701, glgS, plsB, yjcC, feoB, misL, dxr, hemF, rnfG, yhjB, UMN798_1163, UMN798_0394, alkA, nhaA, and lspA, wherein the presence of said at least two mutations is indicative of an infection with an antimicrobial drug, e.g. antibiotic, resistant  Salmonella  strain in said patient.   
     
     
         2 . A method of selecting a treatment of a patient suffering from an infection with a potentially resistant  Salmonella  strain, comprising the steps of:
 a) obtaining or providing a sample containing or suspected of containing at least one  Salmonella  species from the patient;   b) determining the presence of at least one mutation in at least two genes from the group of genes consisting of recN, hemH, UMN798_3428, metE, yijD, UMN798_4831, UMN798_1939, copS, UMN798_0628, UMN798_4878, leuB, recF, emrA, glyQ, dcp, thiH, UMN798_1612, UMN798_2909, UMN798_1680, UMN798_4073, yjbC, nadB, UMN798_3160, hutU, envC, UMN798_3889, UMN798_1629, bcfB, degQ, UMN798_1331, trg, uvrC, polB, hpcD, UMN798_1628, UMN798_1701, glgS, plsB, yjcC, feoB, misL, dxr, hemF, rnfG, yhjB, UMN798_1163, UMN798_0394, alkA, nhaA, and lspA, wherein the presence of said at least two mutations is indicative of a resistance to one or more antimicrobial, e.g. antibiotic, drugs;   c) identifying said at least one or more antimicrobial, e.g. antibiotic, drugs; and   d) selecting one or more antimicrobial, e.g. antibiotic, drugs different from the ones identified in step c) and being suitable for the treatment of a  Salmonella  infection.   
     
     
         3 . The method of one or more of the preceding claims, where the method involves determining the resistance of  Salmonella  to one or more antimicrobial, e.g. antibiotic, drugs. 
     
     
         4 . The method of any one of  claims 1  to  3 , wherein the antimicrobial, e.g. antibiotic, drug is selected from lactam antibiotics and the presence of a mutation in the following genes is determined: recN, hemH, UMN798_3428, metE, yijD, UMN798_4831, UMN798_1939, copS, UMN798_0628, UMN798_4878, leuB, recF, emrA, glyQ, dcp, thiH, UMN798_1612, UMN798_2909, UMN798_1680, UMN798_4073, yjbC, nadB, UMN798_3160, hutU, envC, UMN798_3889, UMN798_1629, bcfB, degQ, UMN798_1331, trg, uvrC, polB, hpcD, UMN798_1628, UMN798_1701, glgS, plsB, yjcC, feoB, misL, dxr, hemF, rnfG, yhjB, UMN798_1163, UMN798_0394, alkA, nhaA, and/or lspA; and/or
 wherein the antimicrobial, e.g. antibiotic, drug is selected from aminoglycoside antibiotics, and the presence of a mutation in the following genes is determined: recN, hemH, UMN798_3428, metE, yijD, UMN798_4831, UMN798_1939, copS, UMN798_0628, UMN798_4878, leuB, recF, emrA, glyQ, dcp, thiH, UMN798_1612, UMN798_2909, UMN798_1680, UMN798_4073, yjbC, nadB, UMN798_3160, hutU, envC, UMN798_3889, UMN798_1629, bcfB, degQ, UMN798_1331, trg, uvrC, polB, hpcD, UMN798_1628, UMN798_1701, glgS, plsB, yjcC, feoB, misL, dxr, hemF, rnfG, yhjB, UMN798_1163, UMN798_0394, alkA, nhaA, and/or lspA; and/or 
 wherein the antimicrobial, e.g. antibiotic, drug is selected from polyketide antibiotics, preferably tetracycline antibiotics, and the presence of a mutation in the following genes is determined: recN, hemH, UMN798_3428, metE, yijD, UMN798_4831, UMN798_1939, copS, UMN798_0628, UMN798_4878, leuB, recF, emrA, glyQ, dcp, thiH, UMN798_1612, UMN798_2909, UMN798_1680, UMN798_4073, yjbC, nadB, UMN798_3160, hutU, envC, UMN798_3889, UMN798_1629, bcfB, UMN798_1331, trg, uvrC, polB, hpcD, UMN798_1628, UMN798_1701, glgS, plsB, yjcC, feoB, misL, dxr, hemF, rnfG, yhjB, UMN798_1163, UMN798_0394, alkA, nhaA, and/or lspA. 
 
     
     
         5 . The method of one or more of the preceding claims, wherein the antimicrobial drug, e.g. antibiotic drug, is selected from the group consisting of Amoxicillin/K Clavulanate (AUG), Ampicillin (AM), Aztreonam (AZT), Cefazolin (CFZ), Cefepime (CPM), Cefotaxime (CFT), Ceftazidime (CAZ), Ceftriaxone (CAX), Cefuroxime (CRM), Cephalotin (CF), Ciprofloxacin (CP), Ertapenem (ETP), Gentamicin (GM), Imipenem (IMP), Levofloxacin (LVX), Meropenem (MER), Piperacillin/Tazobactam (P/T), Ampicillin/Sulbactam (A/S), Tetracycline (TE), Tobramycin (TO), and Trimethoprim/Sulfamethoxazole (T/S). 
     
     
         6 . The method of any one of  claims 1  to  5 , wherein the antibiotic drug is CFZ and a mutation in at least one of the following nucleotide positions is detected with regard to reference genome NC_017046 as annotated at the NCBI: 4779417, 2983118, 1548464, 1574737, 3772654, 1313897; and/or
 wherein the antibiotic drug is GM and a mutation in at least one of the following nucleotide positions is detected with regard to reference genome NC_017046 as annotated at the NCBI: 2840330, 25574, 3536122, 115342, 1148509, 3379140, 4478134, 3686566, 1487086, 3799879, 1163470, 2208848, 46695, 56998, 3335426; and/or 
 wherein the antibiotic drug is CF and a mutation in at least one of the following nucleotide positions is detected with regard to reference genome NC_017046 as annotated at the NCBI: 2833888, 546961, 3334479, 4191057, 4366486, 4724403, 1895588, 1139812, 637461, 4779417, 131219, 4062015, 2983118, 3861998, 1548464, 4397111, 1574737, 1650934, 4436188, 3075942, 855087, 3582301, 3772654, 1590194, 1313897, 1673475, 1994028, 1589819, 1672517, 3976726 3582354, 1673444; and/or 
 wherein the antibiotic drug is TE and a mutation in at least one of the following nucleotide positions is detected with regard to reference genome NC_017046 as annotated at the NCBI: 2833888, 546961, 3334479, 4191057, 4366486, 4724403, 1895588, 1139812, 637461, 4779417, 131219, 4062015, 2983118, 3861998, 1548464, 4397111, 1574737, 2840330, 1650934, 3966175, 4436188, 2780306, 3075942, 855087, 3582301, 3772654, 1590194, 25574, 1313897, 1673475, 1994028, 115342, 1148509, 1589819, 1672517, 3379140, 4478134, 4523874, 3686566, 3976726, 258966, 2558379, 1487086, 3799879, 1163470, 409259, 2208848, 46695, 56998, 3582354, 3335426, 1673444; and/or 
 wherein the antibiotic drug is A/S and a mutation in at least one of the following nucleotide positions is detected with regard to reference genome NC_017046 as annotated at the NCBI: 2833888, 546961, 3334479, 4191057, 4366486, 4724403, 1895588, 1139812, 637461, 4779417, 131219, 4062015, 2983118, 3861998, 1548464, 4397111, 1574737, 2840330, 1650934, 3966175, 4436188, 2780306, 3075942, 855087, 3582301, 3772654, 1590194, 25574, 3536122, 1313897, 1673475, 1994028, 115342, 1148509, 1589819, 1672517, 3379140, 4478134, 4523874, 3686566, 3976726, 258966, 2558379, 1487086, 3799879, 1163470, 409259, 2208848, 46695, 56998, 3582354, 3335426, 1673444; and/or 
 wherein the antibiotic drug is CRM and a mutation in at least one of the following nucleotide positions is detected with regard to reference genome NC_017046 as annotated at the NCBI: 2833888, 546961, 3334479, 4191057, 4366486, 4724403, 1895588, 1139812, 637461, 4779417, 131219, 4062015, 2983118, 3861998, 1548464, 4397111, 1574737, 2840330, 1650934, 3966175, 4436188, 2780306, 3075942, 855087, 3582301, 3772654, 1590194, 25574, 3536122, 1313897, 1673475, 1994028, 115342, 1148509, 1589819, 1672517, 3379140, 4478134, 4523874, 3686566, 3976726, 258966, 2558379, 1487086, 3799879, 1163470, 409259, 2208848, 46695, 56998, 3582354, 3335426, 1673444; and/or 
 wherein the antibiotic drug is P/T and a mutation in at least one of the following nucleotide positions is detected with regard to reference genome NC_017046 as annotated at the NCBI: 2833888, 546961, 3334479, 4191057, 4366486, 4724403, 1895588, 1139812, 637461, 4779417, 131219, 4062015, 2983118, 3861998, 1548464, 4397111, 1574737, 2840330, 1650934, 3966175, 4436188, 2780306, 3075942, 855087, 3582301, 3772654, 1590194, 25574, 3536122, 1313897, 1673475, 1994028, 115342, 1148509, 1589819, 1672517, 3379140, 4478134, 4523874, 3686566, 3976726, 258966, 2558379, 1487086, 3799879, 1163470, 409259, 2208848, 46695, 56998, 3582354, 3335426, 1673444; and/or 
 wherein the antibiotic drug is TO and a mutation in at least one of the following nucleotide positions is detected with regard to reference genome NC_017046 as annotated at the NCBI: 2833888, 546961, 3334479, 4191057, 4366486, 4724403, 1895588, 1139812, 637461, 4779417, 131219, 4062015, 2983118, 3861998, 1548464, 4397111, 1574737, 2840330, 1650934, 3966175, 4436188, 2780306, 3075942, 855087, 3582301, 3772654, 1590194, 25574, 3536122, 1313897, 1673475, 1994028, 115342, 1148509, 1589819, 1672517, 3379140, 4478134, 4523874, 3686566, 3976726, 258966, 2558379, 1487086, 3799879, 1163470, 409259, 2208848, 46695, 56998, 3582354, 3335426, 1673444; and/or 
 wherein the antibiotic drug is AM and a mutation in at least one of the following nucleotide positions is detected with regard to reference genome NC_017046 as annotated at the NCBI: 2833888, 546961, 3334479, 4191057, 4366486, 4724403, 1895588, 1139812, 637461, 4779417, 131219, 4062015, 2983118, 3861998, 1548464, 4397111, 1574737, 2840330, 1650934, 3966175, 4436188, 2780306, 3075942, 855087, 3772654, 25574, 3536122, 1313897, 1994028, 115342, 1148509, 3379140, 4478134, 4523874, 3686566, 3976726, 258966, 2558379, 1487086, 3799879, 1163470, 409259, 2208848, 46695, 56998, 3335426; and/or 
 wherein the antibiotic drug is AUG and a mutation in at least one of the following nucleotide positions is detected with regard to reference genome NC_017046 as annotated at the NCBI: 2833888, 546961, 3334479, 4191057, 4366486, 4724403, 1895588, 1139812, 637461, 4779417, 131219, 4062015, 2983118, 3861998, 1548464, 4397111, 1574737, 2840330, 1650934, 3966175, 4436188, 2780306, 3075942, 855087, 3582301, 3772654, 1590194, 25574, 3536122, 1313897, 1673475, 1994028, 115342, 1148509, 1589819, 1672517, 3379140, 4478134, 4523874, 3686566, 3976726, 258966, 2558379, 1487086, 3799879, 1163470, 409259, 2208848, 46695, 56998, 3582354, 3335426, 1673444. 
 
     
     
         7 . The method of any one of  claims 1  to  6 , wherein the resistance of a bacterial microorganism belonging to the species  Salmonella  against 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 16, 17, 18, 19, 20 or 21 antibiotic drugs is determined. 
     
     
         8 . The method of one or more of the preceding claims, wherein determining the nucleic acid sequence information or the presence of a mutation comprises determining a partial sequence or an entire sequence of the at least two genes. 
     
     
         9 . The method of one or more of the preceding claims, wherein determining the nucleic acid sequence information or the presence of a mutation comprises determining a partial or entire sequence of the genome of the  Salmonella  species, wherein said partial or entire sequence of the genome comprises at least a partial sequence of said at least two genes. 
     
     
         10 . The method of one or more of the preceding claims, wherein determining the nucleic acid sequence information or the presence of a mutation comprises using a next generation sequencing or high throughput sequencing method, preferably wherein a partial or entire genome sequence of the bacterial organism of  Salmonella  species is determined by using a next generation sequencing or high throughput sequencing method. 
     
     
         11 . A method of determining an antimicrobial drug, e.g. antibiotic, resistance profile for bacterial microorganisms of  Salmonella  species, comprising:
 obtaining or providing a first data set of gene sequences of a plurality of clinical isolates of  Salmonella  species;   providing a second data set of antimicrobial drug, e.g. antibiotic, resistance of the plurality of clinical isolates of  Salmonella  species;   aligning the gene sequences of the first data set to at least one, preferably one, reference genome of  Salmonella , and/or assembling the gene sequence of the first data set, at least in part;   analyzing the gene sequences of the first data set for genetic variants to obtain a third data set of genetic variants;   correlating the third data set with the second data set and statistically analyzing the correlation; and   determining the genetic sites in the genome of  Salmonella  associated with antimicrobial drug, e.g. antibiotic, resistance.   
     
     
         12 . A diagnostic method of determining an infection of a patient with  Salmonella  species potentially resistant to antimicrobial drug treatment, comprising the steps of:
 a) obtaining or providing a sample containing or suspected of containing a bacterial microorganism belonging to the species  Salmonella  from the patient;   b) determining the presence of at least one mutation in at least one gene of the bacterial microorganism belonging to the species  Salmonella  as determined by the method of  claim 11 , wherein the presence of said at least one mutation is indicative of an infection with an antimicrobial drug resistant  Salmonella  strain in said patient.   
     
     
         13 . A method of selecting a treatment of a patient suffering from an infection with a potentially resistant  Salmonella  strain, comprising the steps of:
 a) obtaining or providing a sample containing or suspected of containing a bacterial microorganism belonging to the species  Salmonella  from the patient;   b) determining the presence of at least one mutation in at least one gene of the bacterial microorganism belonging to the species  Salmonella  as determined by the method of  claim 11 , wherein the presence of said at least one mutation is indicative of a resistance to one or more antimicrobial drugs;   c) identifying said at least one or more antimicrobial drugs; and   d) selecting one or more antimicrobial drugs different from the ones identified in step c) and being suitable for the treatment of a  Salmonella  infection.   
     
     
         14 . A method of acquiring an antimicrobial drug, e.g. antibiotic, resistance profile for bacterial microorganisms of  Salmonella  species, comprising:
 obtaining or providing a first data set of gene sequences of a clinical isolate of  Salmonella  species;   providing a second data set of antimicrobial drug, e.g. antibiotic, resistance of a plurality of clinical isolates of  Salmonella  species;   aligning the gene sequences of the first data set to at least one, preferably one, reference genome of  Salmonella , and/or assembling the gene sequence of the first data set, at least in part;   analyzing the gene sequences of the first data set for genetic variants to obtain a third data set of genetic variants of the first data set;   correlating the third data set with the second data set and statistically analyzing the correlation; and   determining the genetic sites in the genome of  Salmonella  of the first data set associated with antimicrobial drug, e.g. antibiotic, resistance.   
     
     
         15 . Computer program product comprising computer executable instructions which, when executed, perform a method according to any one of  claims 11  to  14 .